It is widely recognized that binding between proteins is central to virtually all biological processes. With several completed genome sequences as a frame work with which to interpret such interactions, several large scale projects have attempted to define protein interactions for all of the open reading frames of simple organisms including viruses, bacteria, yeast, Drosophila and C. elegans. 
Although other methods of defining protein interactions are possible, the most highly developed method for genome-wide analysis is the original yeast two-hybrid system in which interactions are monitored by the induction of gene expression. This technology can be used in a variety of cell types, including mammalian cells.
Two hybrid analysis works by separating the DNA binding domain (DBD) and activation domain (AD) of a transcriptional activator by cloning their respective coding sequences into separate vectors. One or both DBD and AD coding regions are then fused to many different open reading frames (ORFs), typically from a cDNA library. In the case where the two hybrid system is used in yeast, the DBD and AD vectors can be introduced into the same cell by mating and using DBD and AD vectors that each includes a selectable marker.
If the proteins expressed from the ORFs physically interact, the two halves of the transcriptional activator are brought together and the function of the transcriptional activator is restored. The reconstituted transcriptional activator can then drive expression of a selectable marker, such as a nutritional marker. When the reporter gene is detected, the plasmids with the interacting DBD and AD can be isolated from yeast colonies and the interacting ORF's identified by DNA sequencing.
Large scale projects to define all of the interactions occurring between all of the ˜6,000 open reading frames in yeast have been accomplished using the yeast two hybrid system. However, application of this technology to mammalian genomes, which contain on the order of 10-fold greater complexity, is currently not feasible due to the exponentially greater number of potential interactions that must be scored. Thus, there is a need for an efficient method of identifying genome-wide protein interactions for organisms with complex protein interactions. The present invention meets this need by providing a modification of two-hybrid technology that permits the identification of many pairs of interacting proteins.